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Open data
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Basic information
Entry | Database: PDB / ID: 4h0x | ||||||
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Title | Crystal structure of NAD+-Ia(E380A)-actin complex | ||||||
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![]() | TOXIN/STRUCTURAL PROTEIN / ADP-ribosyltransferase / TOXIN-STRUCTURAL PROTEIN complex | ||||||
Function / homology | ![]() cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / nucleotide binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular region / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsurumura, T. / Oda, M. / Nagahama, M. / Tsuge, H. | ||||||
![]() | ![]() Title: Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Authors: Tsurumura, T. / Tsumori, Y. / Qiu, H. / Oda, M. / Sakurai, J. / Nagahama, M. / Tsuge, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321 KB | Display | ![]() |
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PDB format | ![]() | 256.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4gy2C ![]() 4h03SC ![]() 4h0tC ![]() 4h0vC ![]() 4h0yC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 48161.145 Da / Num. of mol.: 1 / Mutation: E380A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q46220, NAD+-protein-arginine ADP-ribosyltransferase |
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#2: Protein | Mass: 41862.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 7 types, 237 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/LAR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/LAR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAD / | ||||||||
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#4: Chemical | ChemComp-PO4 / | ||||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-ATP / | #8: Chemical | ChemComp-LAR / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.15 % |
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Crystal grow | Temperature: 277.13 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG1500, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.13K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. all: 48818 / Num. obs: 47500 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 9.6 / Num. unique all: 2436 / % possible all: 80 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4H03 Resolution: 2.33→28.58 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.705 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.962 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→28.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.327→2.387 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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